Ok, here is a video split screen of both my phone and my desktop, these are the only devices I own that run Anki. There is no other machine I have ever installed Anki on. I’ve also run this test after syncing both devices and then shutting the phone off. The result is the same.
Even after signing out and ensuring both devices are synced, the issue still happens (the clocks on both machines are synced):
Okay, but how about trying the steps I described above. In particular, forcing a one-way sync in which you select Upload.
Although I guess you could delete the media files the ordinary way, within Anki, instead of the way I described it via the filesystem, as long as you verify that behind the scenes, the filesystem directory does get emptied out of the files in question.
Based on your video, AnkiDroid does seem to be a bystander while all this is happening. Just for reference, is it a recent version?
DAE Said that forces do not effect media in this post: Large Amount of Unused Media Effectively Unremovable? - #8 by dae
Ankidroid is the most recent version from the play store, but even with the phone shut down (it was closed during the syncing), it should not be able to effect anything.
In the beginning of this, I did try to just delete the entire media folder, but that didn’t help.
Okay I’m out of ideas. Hopefully when dae watches the video he will figure out if it fully follows his suggestions.
Just to eliminate possibilities, what about that 1 missing file? Can you download it from somewhere, or instead edit the card(s) that use it, to not use it? Just in case its absence is triggering some glitch?
I seriously doubt it, I have no idea where I would even find it.
Maybe this is it:
https://physicaltherapyreviewer.files.wordpress.com/2015/08/15-aortic-sys-mur-absent-s2-sitting-bell.mp3
(found at Heart Auscultation and Murmurs – Physical Therapy Reviewer)
Click the three vertical dots and select Download.
After adding the file to the collection folder, it still has the same issue 
At least we know that wasn’t it 
All of your devices must be fully in sync before you delete the media. When you sign out, you put them out of sync.
Ok, but not signing out and binning then deleting the media just forces a re-download next sync, even if the phone is off.
If you’re getting the same result whether you sign out or not though, why introduce that as an additional variable against dae’s advice?
Are you sure you have ~30K other files? Your screenshots have captured “Checked” at certain moments as 85K+ and 202K+. (Or am I mistaken and that is related to filesize, not count?)
[Idea 0: Are you using the new backend on AnkiDroid (Settings > Advanced)? Despite the warning message, it’s very stable on 2.16.5. Don’t know if that will help, but it will eliminate another variable. (Enabling the v3 scheduler there will also ensure your scheduler matches between platforms, and eliminate another variable, but seems less likely to help.)]
Idea 1: Have you tried using Check Media on AnkiDroid to delete the files – either instead of or in addition to a Check on AnkiDesktop? Admittedly, there’s some overhead to deleting 27K files if the non-success case is they have to be re-downloaded again 
– but just trying to think of creative ways to get you out of this loop.
Idea 2: Have you tried doing everything that’s been suggested, all in one go (for instance, you seemed to have your add-ons enabled in the video)? Tracking it step-by-step is also more likely to point to exactly where the problem is.
It should be clear to you at some point in that process exactly where it went wrong … or else it could just work!
After experienting around with different email addresses, I found that making any other account appears to solve the issue
I’m not sure what this means. Both phone and desktop have no problem syncing to it and do not have the media issue.
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